1
|
Richard V, Mitsa G, Eshghi A, Chaplygina D, Mohammed Y, Goodlett DR, Zahedi RP, Thevis M, Borchers CH. Establishing Personalized Blood Protein Reference Ranges Using Noninvasive Microsampling and Targeted Proteomics: Implications for Antidoping Strategies. J Proteome Res 2024; 23:1779-1787. [PMID: 38655860 PMCID: PMC11077581 DOI: 10.1021/acs.jproteome.4c00020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/28/2024] [Accepted: 04/05/2024] [Indexed: 04/26/2024]
Abstract
To prevent doping practices in sports, the World Anti-Doping Agency implemented the Athlete Biological Passport (ABP) program, monitoring biological variables over time to indirectly reveal the effects of doping rather than detect the doping substance or the method itself. In the context of this program, a highly multiplexed mass spectrometry-based proteomics assay for 319 peptides corresponding to 250 proteins was developed, including proteins associated with blood-doping practices. "Baseline" expression profiles of these potential biomarkers in capillary blood (dried blood spots (DBS)) were established using multiple reaction monitoring (MRM). Combining DBS microsampling with highly multiplexed MRM assays is the best-suited technology to enhance the effectiveness of the ABP program, as it represents a cost-effective and robust alternative analytical method with high specificity and selectivity of targets in the attomole range. DBS data were collected from 10 healthy athlete volunteers over a period of 140 days (28 time points per participant). These comprehensive findings provide a personalized targeted blood proteome "fingerprint" showcasing that the targeted proteome is unique to an individual and likely comparable to a DNA fingerprint. The results can serve as a baseline for future studies investigating doping-related perturbations.
Collapse
Affiliation(s)
- Vincent
R. Richard
- Segal
Cancer Proteomics Centre, Lady Davis Institute
for Medical Research, Jewish General Hospital, Montréal, Quebec H3T 1E2, Canada
| | - Georgia Mitsa
- Segal
Cancer Proteomics Centre, Lady Davis Institute
for Medical Research, Jewish General Hospital, Montréal, Quebec H3T 1E2, Canada
- Division
of Experimental Medicine, McGill University, Montréal, Quebec H4A 3J1, Canada
| | - Azad Eshghi
- University
of Victoria-Genome BC Proteomics Centre, Victoria, British Columbia V8Z 7X8, Canada
| | - Daria Chaplygina
- Segal
Cancer Proteomics Centre, Lady Davis Institute
for Medical Research, Jewish General Hospital, Montréal, Quebec H3T 1E2, Canada
| | - Yassene Mohammed
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden 2333 ZC, The Netherlands
| | - David R. Goodlett
- University
of Victoria-Genome BC Proteomics Centre, Victoria, British Columbia V8Z 7X8, Canada
| | - Rene P. Zahedi
- Manitoba
Centre for Proteomics and Systems Biology, Winnipeg, Manitoba R3E 3P4, Canada
- Department
of Internal Medicine, University of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
- Department
of Biochemistry and Medical Genetics, University
of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada
- CancerCare
Manitoba Research Institute, Winnipeg, Manitoba R3E 0V9, Canada
| | - Mario Thevis
- Institute
of Biochemistry, Center for Preventive Doping Research, German Sport University Cologne, Cologne 50933, Germany
- European
Monitoring Center for Emerging Doping Agents (EuMoCEDA), Cologne/Bonn 50933, Germany
| | - Christoph H. Borchers
- Segal
Cancer Proteomics Centre, Lady Davis Institute
for Medical Research, Jewish General Hospital, Montréal, Quebec H3T 1E2, Canada
- Division
of Experimental Medicine, McGill University, Montréal, Quebec H4A 3J1, Canada
- Gerald
Bronfman Department of Oncology, McGill
University, Montréal, Quebec H4A 3T2, Canada
- Department
of Pathology, McGill University, Montréal, Quebec H4A 3J1, Canada
| |
Collapse
|
2
|
Zhang AMY, Xia YH, Lin JSH, Chu KH, Wang WCK, Ruiter TJJ, Yang JCC, Chen N, Chhuor J, Patil S, Cen HH, Rideout EJ, Richard VR, Schaeffer DF, Zahedi RP, Borchers CH, Johnson JD, Kopp JL. Hyperinsulinemia acts via acinar insulin receptors to initiate pancreatic cancer by increasing digestive enzyme production and inflammation. Cell Metab 2023; 35:2119-2135.e5. [PMID: 37913768 DOI: 10.1016/j.cmet.2023.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 06/02/2023] [Accepted: 10/06/2023] [Indexed: 11/03/2023]
Abstract
The rising pancreatic cancer incidence due to obesity and type 2 diabetes is closely tied to hyperinsulinemia, an independent cancer risk factor. Previous studies demonstrated reducing insulin production suppressed pancreatic intraepithelial neoplasia (PanIN) pre-cancerous lesions in Kras-mutant mice. However, the pathophysiological and molecular mechanisms remained unknown, and in particular it was unclear whether hyperinsulinemia affected PanIN precursor cells directly or indirectly. Here, we demonstrate that insulin receptors (Insr) in KrasG12D-expressing pancreatic acinar cells are dispensable for glucose homeostasis but necessary for hyperinsulinemia-driven PanIN formation in the context of diet-induced hyperinsulinemia and obesity. Mechanistically, this was attributed to amplified digestive enzyme protein translation, triggering of local inflammation, and PanIN metaplasia in vivo. In vitro, insulin dose-dependently increased acinar-to-ductal metaplasia formation in a trypsin- and Insr-dependent manner. Collectively, our data shed light on the mechanisms connecting obesity-driven hyperinsulinemia and pancreatic cancer development.
Collapse
Affiliation(s)
- Anni M Y Zhang
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Yi Han Xia
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Jeffrey S H Lin
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Ken H Chu
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Wei Chuan K Wang
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Titine J J Ruiter
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Jenny C C Yang
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Nan Chen
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Justin Chhuor
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Shilpa Patil
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Haoning Howard Cen
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Elizabeth J Rideout
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Vincent R Richard
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC H3T 1E2, Canada
| | - David F Schaeffer
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z7, Canada
| | - Rene P Zahedi
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC H3T 1E2, Canada; Department of Internal Medicine, University of Manitoba, Winnipeg, MB R3A 1R9, Canada; Manitoba Centre for Proteomics and Systems Biology, Winnipeg, MB R3E 3P4, Canada
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC H3T 1E2, Canada; Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, QC H4A 3T2, Canada
| | - James D Johnson
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
| | - Janel L Kopp
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
| |
Collapse
|
3
|
Neale Q, Prefontaine A, Battellino T, Mizero B, Yeung D, Spicer V, Budisa N, Perreault H, Zahedi RP, Krokhin OV. Compendium of Chromatographic Behavior of Post-translationally and Chemically Modified Peptides in Bottom-Up Proteomic Experiments. Anal Chem 2023; 95:14634-14642. [PMID: 37739932 DOI: 10.1021/acs.analchem.3c02412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
We have systematically evaluated the chromatographic behavior of post-translationally/chemically modified peptides using data spanning over 70 of the most relevant modifications. These retention properties were measured for standard bottom-up proteomic settings (fully porous C18 separation media, 0.1% formic acid as ion-pairing modifier) using collections of modified/nonmodified peptide pairs. These pairs were generated by spontaneous degradation, chemical or enzymatic treatment, analysis of synthetic peptides, or the cotranslational incorporation of noncanonical proline analogues. In addition, these measurements were validated using external data acquired for synthetic peptides and enzymatically induced citrullination. Working in units of hydrophobicity index (HI, % ACN) and evaluating the average retention shifts (ΔHI) represent the simplest approach to describe the effect of modifications from a didactic point of view. Plotting HI values for modified (y-axis) vs nonmodified (x-axis) counterparts generates unique slope and intercept values for each modification defined by the chemistry of the modifying moiety: its hydrophobicity, size, pKa of ionizable groups, and position of the altered residue. These composition-dependent correlations can be used for coarse incorporation of PTMs into models for prediction of peptide retention. More accurate predictions would require the development of specific sequence-dependent algorithms to predict ΔHI values.
Collapse
Affiliation(s)
- Quinn Neale
- Department of Chemistry, University of Manitoba, 360 Parker Building, Winnipeg R3T 2N2, Manitoba, Canada
| | - Alexandre Prefontaine
- Department of Chemistry, University of Manitoba, 360 Parker Building, Winnipeg R3T 2N2, Manitoba, Canada
| | - Taylor Battellino
- Department of Chemistry, University of Manitoba, 360 Parker Building, Winnipeg R3T 2N2, Manitoba, Canada
| | - Benilde Mizero
- Department of Chemistry, University of Manitoba, 360 Parker Building, Winnipeg R3T 2N2, Manitoba, Canada
| | - Darien Yeung
- Department of Biochemistry and Medical Genetics, University of Manitoba, 336 Basic Medical Sciences Building, 745 Bannatyne Avenue, Winnipeg R3E 0J9, Manitoba, Canada
| | - Victor Spicer
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, 799 JBRC, 715 McDermot Avenue, Winnipeg R3E 3P4, Manitoba, Canada
| | - Nediljko Budisa
- Department of Chemistry, University of Manitoba, 360 Parker Building, Winnipeg R3T 2N2, Manitoba, Canada
| | - Helene Perreault
- Department of Chemistry, University of Manitoba, 360 Parker Building, Winnipeg R3T 2N2, Manitoba, Canada
| | - Rene P Zahedi
- Department of Biochemistry and Medical Genetics, University of Manitoba, 336 Basic Medical Sciences Building, 745 Bannatyne Avenue, Winnipeg R3E 0J9, Manitoba, Canada
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, 799 JBRC, 715 McDermot Avenue, Winnipeg R3E 3P4, Manitoba, Canada
- Department of Internal Medicine, University of Manitoba, 799 JBRC, 715 McDermot Avenue, Winnipeg R3E 3P4, Manitoba, Canada
- CancerCare Manitoba Research Institute, 675 McDermot Avenue, Winnipeg R3E 0 V9, Manitoba, Canada
| | - Oleg V Krokhin
- Department of Biochemistry and Medical Genetics, University of Manitoba, 336 Basic Medical Sciences Building, 745 Bannatyne Avenue, Winnipeg R3E 0J9, Manitoba, Canada
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, 799 JBRC, 715 McDermot Avenue, Winnipeg R3E 3P4, Manitoba, Canada
- Department of Internal Medicine, University of Manitoba, 799 JBRC, 715 McDermot Avenue, Winnipeg R3E 3P4, Manitoba, Canada
| |
Collapse
|
4
|
Abdelkader Y, Perez-Davalos L, LeDuc R, Zahedi RP, Labouta HI. Omics approaches for the assessment of biological responses to nanoparticles. Adv Drug Deliv Rev 2023; 200:114992. [PMID: 37414362 DOI: 10.1016/j.addr.2023.114992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/08/2023] [Accepted: 07/03/2023] [Indexed: 07/08/2023]
Abstract
Nanotechnology has enabled the development of innovative therapeutics, diagnostics, and drug delivery systems. Nanoparticles (NPs) can influence gene expression, protein synthesis, cell cycle, metabolism, and other subcellular processes. While conventional methods have limitations in characterizing responses to NPs, omics approaches can analyze complete sets of molecular entities that change upon exposure to NPs. This review discusses key omics approaches, namely transcriptomics, proteomics, metabolomics, lipidomics and multi-omics, applied to the assessment of biological responses to NPs. Fundamental concepts and analytical methods used for each approach are presented, as well as good practices for omics experiments. Bioinformatics tools are essential to analyze, interpret and visualize large omics data, and to correlate observations in different molecular layers. The authors envision that conducting interdisciplinary multi-omics analyses in future nanomedicine studies will reveal integrated cell responses to NPs at different omics levels, and the incorporation of omics into the evaluation of targeted delivery, efficacy, and safety will improve the development of nanomedicine therapies.
Collapse
Affiliation(s)
- Yasmin Abdelkader
- Unity Health Toronto - St. Michael's Hospital, University of Toronto, 209 Victoria St., Toronto, Ontario M5B 1T8, Canada; College of Pharmacy, Apotex Centre, University of Manitoba, 750 McDermot Av. W, Winnipeg, Manitoba R3E 0T5, Canada; Department of Cell Biology, Biotechnology Research Institute, National Research Centre, 33 El Buhouth St., Cairo 12622, Egypt
| | - Luis Perez-Davalos
- Unity Health Toronto - St. Michael's Hospital, University of Toronto, 209 Victoria St., Toronto, Ontario M5B 1T8, Canada; College of Pharmacy, Apotex Centre, University of Manitoba, 750 McDermot Av. W, Winnipeg, Manitoba R3E 0T5, Canada
| | - Richard LeDuc
- Children's Hospital Research Institute of Manitoba, 513 - 715 McDermot Av. W, Winnipeg, Manitoba R3E 3P4, Canada; Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Av., Winnipeg, Manitoba R3E 0J9, Canada
| | - Rene P Zahedi
- Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Av., Winnipeg, Manitoba R3E 0J9, Canada; Department of Internal Medicine, 715 McDermot Av., Winnipeg, Manitoba R3E 3P4, Canada; Manitoba Centre for Proteomics and Systems Biology, 799 JBRC, 715 McDermot Av., Winnipeg, Manitoba R3E 3P4, Canada; CancerCare Manitoba Research Institute, 675 McDermot Av., Manitoba R3E 0V9, Canada
| | - Hagar I Labouta
- Unity Health Toronto - St. Michael's Hospital, University of Toronto, 209 Victoria St., Toronto, Ontario M5B 1T8, Canada; College of Pharmacy, Apotex Centre, University of Manitoba, 750 McDermot Av. W, Winnipeg, Manitoba R3E 0T5, Canada; Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College St., Toronto, Ontario M5S 3M2, Canada; Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, M5S 3G9, Canada; Faculty of Pharmacy, Alexandria University, 1 Khartoum Square, Azarita, Alexandria, Egypt, 21521.
| |
Collapse
|
5
|
Castillo-Castrejon M, Sankofi BM, Murguia SJ, Udeme AA, Cen HH, Xia YH, Thomas NS, Berry WL, Jones KL, Richard VR, Zahedi RP, Borchers CH, Johnson JD, Wellberg EA. FGF1 supports glycolytic metabolism through the estrogen receptor in endocrine-resistant and obesity-associated breast cancer. Breast Cancer Res 2023; 25:99. [PMID: 37608351 PMCID: PMC10463730 DOI: 10.1186/s13058-023-01699-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 08/16/2023] [Indexed: 08/24/2023] Open
Abstract
BACKGROUND Obesity increases breast cancer risk and breast cancer-specific mortality, particularly for people with estrogen receptor (ER)-positive tumors. Body mass index (BMI) is used to define obesity, but it may not be the best predictor of breast cancer risk or prognosis on an individual level. Adult weight gain is an independent indicator of breast cancer risk. Our previous work described a murine model of obesity, ER-positive breast cancer, and weight gain and identified fibroblast growth factor receptor (FGFR) as a potential driver of tumor progression. During adipose tissue expansion, the FGF1 ligand is produced by hypertrophic adipocytes as a stimulus to stromal preadipocytes that proliferate and differentiate to provide additional lipid storage capacity. In breast adipose tissue, FGF1 production may stimulate cancer cell proliferation and tumor progression. METHODS We explored the effects of FGF1 on ER-positive endocrine-sensitive and resistant breast cancer and compared that to the effects of the canonical ER ligand, estradiol. We used untargeted proteomics, specific immunoblot assays, gene expression profiling, and functional metabolic assessments of breast cancer cells. The results were validated in tumors from obese mice and breast cancer datasets from women with obesity. RESULTS FGF1 stimulated ER phosphorylation independently of estradiol in cells that grow in obese female mice after estrogen deprivation treatment. Phospho- and total proteomic, genomic, and functional analyses of endocrine-sensitive and resistant breast cancer cells show that FGF1 promoted a cellular phenotype characterized by glycolytic metabolism. In endocrine-sensitive but not endocrine-resistant breast cancer cells, mitochondrial metabolism was also regulated by FGF1. Comparison of gene expression profiles indicated that tumors from women with obesity shared hallmarks with endocrine-resistant breast cancer cells. CONCLUSIONS Collectively, our data suggest that one mechanism by which obesity and weight gain promote breast cancer progression is through estrogen-independent ER activation and cancer cell metabolic reprogramming, partly driven by FGF/FGFR. The first-line treatment for many patients with ER-positive breast cancer is inhibition of estrogen synthesis using aromatase inhibitors. In women with obesity who are experiencing weight gain, locally produced FGF1 may activate ER to promote cancer cell metabolic reprogramming and tumor progression independently of estrogen.
Collapse
Affiliation(s)
- Marisol Castillo-Castrejon
- Department of Pathology, University of Oklahoma Health Sciences Center, 975 NE 10th Street BRC 309, Oklahoma City, OK, 73104, USA
| | - Barbara Mensah Sankofi
- Department of Pathology, University of Oklahoma Health Sciences Center, 975 NE 10th Street BRC 309, Oklahoma City, OK, 73104, USA
| | - Stevi Johnson Murguia
- Department of Pathology, University of Oklahoma Health Sciences Center, 975 NE 10th Street BRC 309, Oklahoma City, OK, 73104, USA
| | - Abasi-Ama Udeme
- Department of Pathology, University of Oklahoma Health Sciences Center, 975 NE 10th Street BRC 309, Oklahoma City, OK, 73104, USA
| | - Hoaning Howard Cen
- Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Yi Han Xia
- Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Nisha S Thomas
- Department of Pathology, University of Oklahoma Health Sciences Center, 975 NE 10th Street BRC 309, Oklahoma City, OK, 73104, USA
| | - William L Berry
- Department of Pathology, University of Oklahoma Health Sciences Center, 975 NE 10th Street BRC 309, Oklahoma City, OK, 73104, USA
| | - Kenneth L Jones
- Department of Pathology, University of Oklahoma Health Sciences Center, 975 NE 10th Street BRC 309, Oklahoma City, OK, 73104, USA
| | - Vincent R Richard
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital and McGill University, Montreal, QC, Canada
| | - Rene P Zahedi
- Manitoba Centre for Proteomics and Systems Biology, Winnipeg, MB, R3E 3P4, Canada
- Department of Internal Medicine, University of Manitoba, Winnipeg, MB, R3E 3P4, Canada
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada
- CancerCare Manitoba Research Institute, Winnipeg, MB, R3E 0V9, Canada
| | - Christoph H Borchers
- Manitoba Centre for Proteomics and Systems Biology, Winnipeg, MB, R3E 3P4, Canada
- Gerald Bronfman Department of Oncology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, H3T 1E2, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, H4A 3J1, Canada
- Department of Pathology, McGill University, Montreal, QC, H3A 2B4, Canada
| | - James D Johnson
- Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Elizabeth A Wellberg
- Department of Pathology, University of Oklahoma Health Sciences Center, 975 NE 10th Street BRC 309, Oklahoma City, OK, 73104, USA.
| |
Collapse
|
6
|
Solari FA, Krahn D, Swieringa F, Verhelst S, Rassaf T, Tasdogan A, Zahedi RP, Lorenz K, Renné T, Heemskerk JWM, Sickmann A. Multi-omics approaches to study platelet mechanisms. Curr Opin Chem Biol 2023; 73:102253. [PMID: 36689818 DOI: 10.1016/j.cbpa.2022.102253] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/17/2022] [Accepted: 11/27/2022] [Indexed: 01/22/2023]
Abstract
Platelets are small anucleate cell fragments (2-4 μm in diameter) in the blood, which play an essential role in thrombosis and hemostasis. Genetic or acquired platelet dysfunctions are linked to bleeding, increased risk of thromboembolic events and cardiovascular diseases. Advanced proteomic approaches may pave the way to a better understanding of the roles of platelets in hemostasis, and pathophysiological processes such as inflammation, metastatic spread and thrombosis. Further insights into the molecular biology of platelets are crucial to aid drug development and identify diagnostic markers of platelet activation. Platelet activation is known to be an extremely rapid process and involves multiple post-translational mechanisms at sub second time scale, including proteolysis and phosphorylation. Multi-omics technologies and biochemical approaches can be exploited to precisely probe and define these posttranslational pathways. Notably, the absence of a nucleus in platelets significantly reduces the number of present proteins, simplifying mass spectrometry-based proteomics and metabolomics approaches.
Collapse
Affiliation(s)
- Fiorella A Solari
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44143, Dortmund, Germany
| | - Daniel Krahn
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44143, Dortmund, Germany
| | - Frauke Swieringa
- Synapse Research Institute Maastricht, 6217 KD, Maastricht, the Netherlands
| | - Steven Verhelst
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44143, Dortmund, Germany; Department of Cellular and Molecular Medicine, KU Leuven, University of Leuven, Leuven, Belgium
| | - Tienush Rassaf
- Clinic for Cardiology and Angiology, University Hospital Essen, Essen, Germany
| | - Alpaslan Tasdogan
- Department of Dermatology, University Hospital Essen & German Cancer Consortium, Partner Site, Essen, Germany
| | - Rene P Zahedi
- Department of Internal Medicine, University of Manitoba, Canada
| | - Kristina Lorenz
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44143, Dortmund, Germany; Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany
| | - Thomas Renné
- Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44143, Dortmund, Germany; Medizinische Fakultät, Ruhr-Universität Bochum, Bochum, Germany; Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, United Kingdom.
| |
Collapse
|
7
|
Prabhu SA, Moussa O, Gonçalves C, LaPierre JH, Chou H, Huang F, Richard VR, Ferruzo PYM, Guettler EM, Soria-Bretones I, Kirby L, Gagnon N, Su J, Silvester J, Krisna SS, Rose AAN, Sheppard KE, Cescon DW, Mallette FA, Zahedi RP, Borchers CH, Del Rincon SV, Miller WH. Inhibition of the MNK1/2-eIF4E Axis Augments Palbociclib-Mediated Antitumor Activity in Melanoma and Breast Cancer. Mol Cancer Ther 2023; 22:192-204. [PMID: 36722142 DOI: 10.1158/1535-7163.mct-22-0092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 10/12/2022] [Accepted: 12/08/2022] [Indexed: 02/02/2023]
Abstract
Aberrant cell-cycle progression is characteristic of melanoma, and CDK4/6 inhibitors, such as palbociclib, are currently being tested for efficacy in this disease. Despite the promising nature of CDK4/6 inhibitors, their use as single agents in melanoma has shown limited clinical benefit. Herein, we discovered that treatment of tumor cells with palbociclib induces the phosphorylation of the mRNA translation initiation factor eIF4E. When phosphorylated, eIF4E specifically engenders the translation of mRNAs that code for proteins involved in cell survival. We hypothesized that cancer cells treated with palbociclib use upregulated phosphorylated eIF4E (phospho-eIF4E) to escape the antitumor benefits of this drug. Indeed, we found that pharmacologic or genetic disruption of MNK1/2 activity, the only known kinases for eIF4E, enhanced the ability of palbociclib to decrease clonogenic outgrowth. Moreover, a quantitative proteomics analysis of melanoma cells treated with combined MNK1/2 and CDK4/6 inhibitors showed downregulation of proteins with critical roles in cell-cycle progression and mitosis, including AURKB, TPX2, and survivin. We also observed that palbociclib-resistant breast cancer cells have higher basal levels of phospho-eIF4E, and that treatment with MNK1/2 inhibitors sensitized these palbociclib-resistant cells to CDK4/6 inhibition. In vivo we demonstrate that the combination of MNK1/2 and CDK4/6 inhibition significantly increases the overall survival of mice compared with either monotherapy. Overall, our data support MNK1/2 inhibitors as promising drugs to potentiate the antineoplastic effects of palbociclib and overcome therapy-resistant disease.
Collapse
Affiliation(s)
- Sathyen A Prabhu
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec, Canada
- Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
| | - Omar Moussa
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec, Canada
- Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
| | | | - Judith H LaPierre
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec, Canada
- Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
| | - Hsiang Chou
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec, Canada
| | - Fan Huang
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec, Canada
- Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
| | - Vincent R Richard
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Pault Y M Ferruzo
- Centre de recherche de l'Hôpital Maisonneuve-Rosemont, Montréal, Québec, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | | | - Isabel Soria-Bretones
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Laura Kirby
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Natascha Gagnon
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec, Canada
| | - Jie Su
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec, Canada
| | - Jennifer Silvester
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | | | - April A N Rose
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec, Canada
- Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montréal, Québec, Canada
| | - Karen E Sheppard
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, Australia
| | - David W Cescon
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- University of Toronto, Toronto, Ontario, Canada
| | - Frédérick A Mallette
- Centre de recherche de l'Hôpital Maisonneuve-Rosemont, Montréal, Québec, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
- Department of Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Rene P Zahedi
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- McGill Centre for Translational Research in Cancer, McGill University, Montréal, Québec, Canada
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montréal, Québec, Canada
- McGill Centre for Translational Research in Cancer, McGill University, Montréal, Québec, Canada
| | - Sonia V Del Rincon
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec, Canada
- Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
- McGill Centre for Translational Research in Cancer, McGill University, Montréal, Québec, Canada
| | - Wilson H Miller
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec, Canada
- Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
- McGill Centre for Translational Research in Cancer, McGill University, Montréal, Québec, Canada
| |
Collapse
|
8
|
Lacasse V, Richard V, Wang H, Mitsa G, Poetz O, Papadakis AI, Elchebly M, Cohen V, Agulnik JS, Batist G, Zahedi RP, Borchers CH, Spatz A. Immuno-multiple reaction monitoring (iMRM) for quantitation of PD-L1 and PD-1-signaling proteins in non-small cell lung carcinoma (NSCLC). J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.2627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
2627 Background: More accurate predictive biomarkers of response to checkpoint inhibitors (CPIs) still is a major unmet need in oncology. PD-L1 immunohistochemistry (IHC) limitations include its analytical variability and the post-translational modifications of PD-1 signaling-associated proteins like glycosylation. Moreover, PD-L1 IHC is an imperfect surrogate of the tumor immune microenvironment, and immunoscoring is important but difficult to assess in a clinical setting. Proteomic based technologies can overcome these challenges, but the low concentration of these proteins and the presence of high background noise in formalin-fixed paraffin embedded (FFPE) tumors were limiting obstacles. In this study, we evaluate the benefit of a new approach we used with anti-peptide antibodies to purify surrogate peptides, while liquid chromatography (LC) was coupled to multiple reaction monitoring mass spectrometry (iMRM) to improve specificity and precision of protein quantitation. Methods: To determine the concentration of PD-L1, PD-1, PD-L2, NT5E, LCK and ZAP70, we used unique and well detectable proteolytic peptides as surrogates. In a refined protocol, we optimized protein extraction and digestion, peptide immuno-enrichment, LC and MRM parameters to maximize recovery, increase target-specific signal and reduce noise. Plus, we assessed the glycosylation status of PD-L1, PD-L2, and PD-1. The entire workflow was fully validated using 31 NSCLC FFPE tumors. PD-L1 quantitation by iMRM was compared to PD-L1 IHC clone 22C3. Results: On average, 71±29 µg (n = 52) of protein could be extracted from each 1–3 mm3 NSCLC tumor FFPE core. The optimized iMRM method allowed the quantitation of PD-L1 and PD-1 down to 21 amol on-column. Inter- and intra-day repeatability were well below FDA guidelines (coefficients of variation [CV] < 20%) with average CVs of 5.2±4.0% (intra-day) and 4.5±2.6% (inter-day). Sample storage had no significant effect on peptide quantitation. The final multiplexed iMRM assay enables quantitation all targets and glycosylation states for > 40 samples in only 3 days (including external calibration and quality controls) and was used to quantify the PD-1/PD-L1 axis proteins successfully in all 31 NSCLC FFPE tumors. PD-L1 expression ranged from 2 amol/μg to 61 amol/μg of total protein. As expected, iMRM results correlated moderately (R = 0.56, ρ < 0.001) with PD-L1 IHC. PD-L1 glycosylation status ranged from 99.9±0.2%, and therefore did not explain the discrepancies between IHC and iMRM for these samples. Conclusions: Herein a robust iMRM workflow was developed for the quantitation of the PD-1/PD-L1 axis in FFPE. This proof-of-concept supports that MS-based assay can provide otherwise unavailable data (e.g., PD-L1 concentration, glycosylation status). CPI treated patient tumors are being currently processed to validate the predictive value of the assay.
Collapse
Affiliation(s)
- Vincent Lacasse
- Lady Davis Institute & McGill University, Montreal, QC, Canada
| | | | - Hangjun Wang
- Jewish General Hospital, Lady Davis Institute, McGill University Health Center, McGill University, Montréal, QC, Canada
| | - Georgia Mitsa
- Lady Davis Institute & McGill University, Montreal, QC, Canada
| | | | | | | | - Victor Cohen
- McGill University & Jewish General Hospital, Montreal, QC, Canada
| | - Jason S. Agulnik
- Jewish General Hospital, McGill University, Montréal, QC, Canada
| | - Gerald Batist
- Segal Cancer Centre-Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Rene P. Zahedi
- Lady Davis Institute & Skolkovo Institute of Science and Technology, Montreal, QC, Canada
| | - Christoph H. Borchers
- Jewish General Hospital, Lady Davis Institute, McGill University, Montréal, QC, Canada
| | - Alan Spatz
- Jewish General Hospital, Lady Davis Institute, McGill University Health Center, McGill University, Montréal, QC, Canada
| |
Collapse
|
9
|
Kösters M, Leufken J, Schulze S, Sugimoto K, Klein J, Zahedi RP, Hippler M, Leidel SA, Fufezan C. pymzML v2.0: introducing a highly compressed and seekable gzip format. Bioinformatics 2019; 34:2513-2514. [PMID: 29394323 DOI: 10.1093/bioinformatics/bty046] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 01/30/2018] [Indexed: 11/13/2022] Open
Abstract
Motivation In the new release of pymzML (v2.0), we have optimized the speed of this established tool for mass spectrometry data analysis to adapt to increasing amounts of data in mass spectrometry. Thus, we integrated faster libraries for numerical calculations, improved data retrieving algorithms and have optimized the source code. Importantly, to adapt to rapidly growing file sizes, we developed a generalizable compression scheme for very fast random access and applied this concept to mzML files to retrieve spectral data. Results pymzML performs at par with established C programs when it comes to processing times. However, it offers the versatility of a scripting language, while adding unprecedented fast random access to compressed files. Additionally, we designed our compression scheme in such a general way that it can be applied to any field where fast random access to large data blocks in compressed files is desired. Availability and implementation pymzML is freely available on https://github.com/pymzML/pymzML under GPL license. pymzML requires Python3.4+ and optionally numpy. Documentation available on http://pymzml.readthedocs.io.
Collapse
Affiliation(s)
- M Kösters
- Institute of Plant Biology and Biotechnology, WWU Münster, Münster, Germany
| | - J Leufken
- Institute of Plant Biology and Biotechnology, WWU Münster, Münster, Germany.,Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - S Schulze
- Institute of Plant Biology and Biotechnology, WWU Münster, Münster, Germany
| | - K Sugimoto
- Institute of Plant Biology and Biotechnology, WWU Münster, Münster, Germany
| | - J Klein
- Bioinformatics Program, Boston University, One Silber Way, Boston, MA, USA
| | - R P Zahedi
- Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, 5100 de Maisonneuve Boulevard West, Suite 720, Montreal, Quebec, Canada.,Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Côte-Sainte-Catherine Road, Montreal, Quebec, Canada
| | - M Hippler
- Institute of Plant Biology and Biotechnology, WWU Münster, Münster, Germany
| | - S A Leidel
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - C Fufezan
- Institute of Plant Biology and Biotechnology, WWU Münster, Münster, Germany.,Cellzome A GSK Company, Heidelberg, Germany
| |
Collapse
|
10
|
Kopczynski D, Coman C, Zahedi RP, Lorenz K, Sickmann A, Ahrends R. Multi-OMICS: a critical technical perspective on integrative lipidomics approaches. Biochim Biophys Acta Mol Cell Biol Lipids 2017; 1862:808-811. [PMID: 28193460 DOI: 10.1016/j.bbalip.2017.02.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 02/03/2017] [Accepted: 02/06/2017] [Indexed: 02/06/2023]
Abstract
During the past decades, high-throughput approaches for analyzing different molecular classes such as nucleic acids, proteins, metabolites, and lipids have grown rapidly. These approaches became powerful tools for getting a fundamental understanding of biological systems. Considering each approach and its results separately, relations and causal connections between these classes have no chance to be revealed, since only separate molecular snapshots are provided. Only a combined approach, not fully established yet, with the integration of the corresponding data, might yield a comprehensive and complete understanding of biological processes, such as crosstalk and interactions in signaling pathways. Taking two or more omics-methods into consideration for analysis is referred to as a multi-omics approach, which is gradually evolving. In this critical note, we briefly discuss the relevance, challenges, current state, and potential of data integration from multi-omics approaches, with a special focus on lipidomics analysis, listing the advantages and gaps in this field. This article is part of a Special Issue entitled: BBALIP_Lipidomics Opinion Articles edited by Sepp Kohlwein.
Collapse
Affiliation(s)
- Dominik Kopczynski
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, Dortmund, Germany
| | - Cristina Coman
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, Dortmund, Germany
| | - Rene P Zahedi
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, Dortmund, Germany
| | - Kristina Lorenz
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, Dortmund, Germany; West German Heart and Vascular Center Essen, University Hospital Essen, Essen, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, Dortmund, Germany; Medizinische Fakultät, Medizinische Proteom-Center (MPC), Ruhr-Universität Bochum, Bochum, Germany; Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, Scotland, UK
| | - Robert Ahrends
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, Dortmund, Germany.
| |
Collapse
|
11
|
Gavriljuk K, Schartner J, Seidel H, Dickhut C, Zahedi RP, Hedberg C, Kötting C, Gerwert K. Unraveling the Phosphocholination Mechanism of the Legionella pneumophila Enzyme AnkX. Biochemistry 2016; 55:4375-85. [PMID: 27404583 DOI: 10.1021/acs.biochem.6b00524] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The intracellular pathogen Legionella pneumophila infects lung macrophages and injects numerous effector proteins into the host cell to establish a vacuole for proliferation. The necessary interference with vesicular trafficking of the host is achieved by modulation of the function of Rab GTPases. The effector protein AnkX chemically modifies Rab1b and Rab35 by covalent phosphocholination of serine or threonine residues using CDP-choline as a donor. So far, the phosphoryl transfer mechanism and the relevance of observed autophosphocholination of AnkX remained disputable. We designed tailored caged compounds to make this type of enzymatic reaction accessible for time-resolved Fourier transform infrared difference spectroscopy. By combining spectroscopic and biochemical methods, we determined that full length AnkX is autophosphocholinated at Ser521, Thr620, and Thr943. However, autophosphocholination loses specificity for these sites in shortened constructs and does not appear to be relevant for the catalysis of the phosphoryl transfer. In contrast, transient phosphocholination of His229 in the conserved catalytic motif might exist as a short-lived reaction intermediate. Upon substrate binding, His229 is deprotonated and locked in this state, being rendered capable of a nucleophilic attack on the pyrophosphate moiety of the substrate. The proton that originated from His229 is transferred to a nearby carboxylic acid residue. Thus, our combined findings support a ping-pong mechanism involving phosphocholination of His229 and subsequent transfer of phosphocholine to the Rab GTPase. Our approach can be extended to the investigation of further nucleotidyl transfer reactions, which are currently of reemerging interest in regulatory pathways of host-pathogen interactions.
Collapse
Affiliation(s)
- Konstantin Gavriljuk
- Department of Biophysics, Ruhr-Universität Bochum , Universitätsstrasse 150, 44801 Bochum, Germany
| | - Jonas Schartner
- Department of Biophysics, Ruhr-Universität Bochum , Universitätsstrasse 150, 44801 Bochum, Germany
| | - Hans Seidel
- Department of Biophysics, Ruhr-Universität Bochum , Universitätsstrasse 150, 44801 Bochum, Germany
| | - Clarissa Dickhut
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V. , Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany
| | - Rene P Zahedi
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V. , Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany
| | - Christian Hedberg
- Department of Chemistry and Umeå Center for Microbial Research, Umeå University , SE-90187 Umeå, Sweden
| | - Carsten Kötting
- Department of Biophysics, Ruhr-Universität Bochum , Universitätsstrasse 150, 44801 Bochum, Germany
| | - Klaus Gerwert
- Department of Biophysics, Ruhr-Universität Bochum , Universitätsstrasse 150, 44801 Bochum, Germany
| |
Collapse
|
12
|
Huelsemann MF, Patz M, Beckmann L, Brinkmann K, Otto T, Fandrey J, Becker HJ, Theurich S, von Bergwelt-Baildon M, Pallasch CP, Zahedi RP, Kashkar H, Reinhardt HC, Hallek M, Wendtner CM, Frenzel LP. Hypoxia-induced p38 MAPK activation reduces Mcl-1 expression and facilitates sensitivity towards BH3 mimetics in chronic lymphocytic leukemia. Leukemia 2014; 29:981-4. [PMID: 25376373 DOI: 10.1038/leu.2014.320] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- M F Huelsemann
- 1] Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany [2] Center of Integrated Oncology, University Hospital of Cologne, Cologne, Germany [3] Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University Hospital of Cologne, Cologne, Germany
| | - M Patz
- 1] Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany [2] Center of Integrated Oncology, University Hospital of Cologne, Cologne, Germany [3] Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University Hospital of Cologne, Cologne, Germany
| | - L Beckmann
- 1] Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany [2] Center of Integrated Oncology, University Hospital of Cologne, Cologne, Germany [3] Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University Hospital of Cologne, Cologne, Germany
| | - K Brinkmann
- 1] Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University Hospital of Cologne, Cologne, Germany [2] Institute for Medical Microbiology, Immunology and Hygiene, University Hospital of Cologne, Cologne, Germany
| | - T Otto
- Institute of Physiology, University of Duisburg-Essen, Essen, Germany
| | - J Fandrey
- Institute of Physiology, University of Duisburg-Essen, Essen, Germany
| | - H J Becker
- 1] Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany [2] Center of Integrated Oncology, University Hospital of Cologne, Cologne, Germany
| | - S Theurich
- 1] Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany [2] Center of Integrated Oncology, University Hospital of Cologne, Cologne, Germany
| | - M von Bergwelt-Baildon
- 1] Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany [2] Center of Integrated Oncology, University Hospital of Cologne, Cologne, Germany
| | - C P Pallasch
- 1] Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany [2] Center of Integrated Oncology, University Hospital of Cologne, Cologne, Germany [3] Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University Hospital of Cologne, Cologne, Germany
| | - R P Zahedi
- Leibniz-Institute for Analytical Sciences-ISAS-e.V., Dortmund, Germany
| | - H Kashkar
- 1] Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University Hospital of Cologne, Cologne, Germany [2] Institute for Medical Microbiology, Immunology and Hygiene, University Hospital of Cologne, Cologne, Germany
| | - H C Reinhardt
- 1] Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany [2] Center of Integrated Oncology, University Hospital of Cologne, Cologne, Germany [3] Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University Hospital of Cologne, Cologne, Germany
| | - M Hallek
- 1] Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany [2] Center of Integrated Oncology, University Hospital of Cologne, Cologne, Germany [3] Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University Hospital of Cologne, Cologne, Germany
| | - C M Wendtner
- 1] Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany [2] Center of Integrated Oncology, University Hospital of Cologne, Cologne, Germany [3] Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University Hospital of Cologne, Cologne, Germany [4] Department I of Internal Medicine, Klinikum Schwabing, Munich, Germany
| | - L P Frenzel
- 1] Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany [2] Center of Integrated Oncology, University Hospital of Cologne, Cologne, Germany [3] Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University Hospital of Cologne, Cologne, Germany
| |
Collapse
|
13
|
Subramanian H, Zahedi RP, Sickmann A, Walter U, Gambaryan S. Phosphorylation of CalDAG-GEFI by protein kinase A prevents Rap1b activation. J Thromb Haemost 2013; 11:1574-82. [PMID: 23611601 DOI: 10.1111/jth.12271] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 04/17/2013] [Indexed: 11/24/2022]
Abstract
BACKGROUND Signaling via protein kinase A (PKA) and protein kinase G (PKG) is critical for maintaining platelets in the resting state. Both kinases down-regulate the activity of the small GTPase Rap1b, a critical signaling switch for integrin activation and platelet aggregation. However, the mechanism of Rap1b regulation by PKA and PKG is largely unknown. OBJECTIVE To identify the PKA phosphorylation sites in calcium and diacylglycerol-regulated guanine nucleotide exchange factor I (CalDAG-GEFI), the main GEF for Rap1b in platelets, and the effect of CalDAG-GEFI phosphorylation in Rap1b activation. METHODS The phosphorylation sites in CalDAG-GEFI were identified by radio-active phosphate incorporation assay and mass spectrometry. Phospho-antibody was developed to detect CalDAG-GEFI phosphorylation in Western blots. Rap1b activation was detected by Rap1-GTP pull-down assay. RESULTS S587 was identified as the major PKA phosphorylation site in CalDAG-GEFI, while S116/117 was weakly phosphorylated. Phosphorylation of S587 correlated with the inhibitory effect of PKA on Rap1b activation in platelets. In HEK293 cells, expression of a phospho-mimetic mutant of CalDAG-GEFI (S587D) abolished agonist-induced Rap1b activation. Mutation of S587 to alanine partially reversed the inhibitory effect of PKA signaling on Rap1b activation, while mutation of S116, S117 and S587 to alanine completely abolished the inhibitory effect of PKA on Rap1b activation. CONCLUSION Our study strongly suggests that phosphorylation of CalDAG-GEFI is a critical mechanism by which PKA controls Rap1b-dependent platelet aggregation.
Collapse
Affiliation(s)
- H Subramanian
- Institute of Clinical Biochemistry and Pathobiochemistry, University of Wuerzburg, Wuerzburg, Germany
| | | | | | | | | |
Collapse
|
14
|
Sanges C, Scheuermann C, Zahedi RP, Sickmann A, Lamberti A, Migliaccio N, Baljuls A, Marra M, Zappavigna S, Reinders J, Rapp U, Abbruzzese A, Caraglia M, Arcari P. Erratum: Raf kinases mediate the phosphorylation of eukaryotic translation elongation factor 1A and regulate its stability in eukaryotic cells. Cell Death Dis 2012. [PMCID: PMC3366089 DOI: 10.1038/cddis.2012.67] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
15
|
Sanges C, Scheuermann C, Zahedi RP, Sickmann A, Lamberti A, Migliaccio N, Baljuls A, Marra M, Zappavigna S, Reinders J, Rapp U, Abbruzzese A, Caraglia M, Arcari P. Raf kinases mediate the phosphorylation of eukaryotic translation elongation factor 1A and regulate its stability in eukaryotic cells. Cell Death Dis 2012; 3:e276. [PMID: 22378069 PMCID: PMC3317347 DOI: 10.1038/cddis.2012.16] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We identified eukaryotic translation elongation factor 1A (eEF1A) Raf-mediated phosphorylation sites and defined their role in the regulation of eEF1A half-life and of apoptosis of human cancer cells. Mass spectrometry identified in vitro S21 and T88 as phosphorylation sites mediated by B-Raf but not C-Raf on eEF1A1 whereas S21 was phosphorylated on eEF1A2 by both B- and C-Raf. Interestingly, S21 belongs to the first eEF1A GTP/GDP-binding consensus sequence. Phosphorylation of S21 was strongly enhanced when both eEF1A isoforms were preincubated prior the assay with C-Raf, suggesting that the eEF1A isoforms can heterodimerize thus increasing the accessibility of S21 to the phosphate. Overexpression of eEF1A1 in COS 7 cells confirmed the phosphorylation of T88 also in vivo. Compared with wt, in COS 7 cells overexpressed phosphodeficient (A) and phospho-mimicking (D) mutants of eEF1A1 (S21A/D and T88A/D) and of eEF1A2 (S21A/D), resulted less stable and more rapidly proteasome degraded. Transfection of S21 A/D eEF1A mutants in H1355 cells increased apoptosis in comparison with the wt isoforms. It indicates that the blockage of S21 interferes with or even supports C-Raf induced apoptosis rather than cell survival. Raf-mediated regulation of this site could be a crucial mechanism involved in the functional switching of eEF1A between its role in protein biosynthesis and its participation in other cellular processes.
Collapse
Affiliation(s)
- C Sanges
- Department of Biochemistry and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Polzien L, Baljuls A, Rennefahrt UEE, Fischer A, Schmitz W, Zahedi RP, Sickmann A, Metz R, Albert S, Benz R, Hekman M, Rapp UR. Identification of novel in vivo phosphorylation sites of the human proapoptotic protein BAD: pore-forming activity of BAD is regulated by phosphorylation. J Biol Chem 2009; 284:28004-28020. [PMID: 19667065 DOI: 10.1074/jbc.m109.010702] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
BAD is a proapoptotic member of the Bcl-2 protein family that is regulated by phosphorylation in response to survival factors. Although much attention has been devoted to the identification of phosphorylation sites in murine BAD, little data are available with respect to phosphorylation of human BAD protein. Using mass spectrometry, we identified here besides the established phosphorylation sites at serines 75, 99, and 118 several novel in vivo phosphorylation sites within human BAD (serines 25, 32/34, 97, and 124). Furthermore, we investigated the quantitative contribution of BAD targeting kinases in phosphorylating serine residues 75, 99, and 118. Our results indicate that RAF kinases represent, besides protein kinase A, PAK, and Akt/protein kinase B, in vivo BAD-phosphorylating kinases. RAF-induced phosphorylation of BAD was reduced to control levels using the RAF inhibitor BAY 43-9006. This phosphorylation was not prevented by MEK inhibitors. Consistently, expression of constitutively active RAF suppressed apoptosis induced by BAD and the inhibition of colony formation caused by BAD could be prevented by RAF. In addition, using the surface plasmon resonance technique, we analyzed the direct consequences of BAD phosphorylation by RAF with respect to association with 14-3-3 and Bcl-2/Bcl-X(L) proteins. Phosphorylation of BAD by active RAF promotes 14-3-3 protein association, in which the phosphoserine 99 represented the major binding site. Finally, we show here that BAD forms channels in planar bilayer membranes in vitro. This pore-forming capacity was dependent on phosphorylation status and interaction with 14-3-3 proteins. Collectively, our findings provide new insights into the regulation of BAD function by phosphorylation.
Collapse
Affiliation(s)
- Lisa Polzien
- Institute for Medical Radiation and Cell Research, University of Wuerzburg, 97078 Wuerzburg
| | - Angela Baljuls
- Institute for Medical Radiation and Cell Research, University of Wuerzburg, 97078 Wuerzburg
| | - Ulrike E E Rennefahrt
- Institute for Medical Radiation and Cell Research, University of Wuerzburg, 97078 Wuerzburg
| | - Andreas Fischer
- Institute for Medical Radiation and Cell Research, University of Wuerzburg, 97078 Wuerzburg
| | - Werner Schmitz
- Institute of Physiological Chemistry, University of Wuerzburg, 97078 Wuerzburg
| | - Rene P Zahedi
- Institute for Analytical Sciences, Department of Bioanalytics, 44139 Dortmund
| | - Albert Sickmann
- Institute for Analytical Sciences, Department of Bioanalytics, 44139 Dortmund; Medical Proteome Center, Ruhr University of Bochum, 44801 Bochum, Germany
| | - Renate Metz
- Institute for Medical Radiation and Cell Research, University of Wuerzburg, 97078 Wuerzburg
| | - Stefan Albert
- Julius-von-Sachs Institute for Biosciences, University of Wuerzburg, 97078 Wuerzburg
| | - Roland Benz
- Institute of Biotechnology, University of Wuerzburg, 97078 Wuerzburg
| | - Mirko Hekman
- Institute for Medical Radiation and Cell Research, University of Wuerzburg, 97078 Wuerzburg
| | - Ulf R Rapp
- Institute for Medical Radiation and Cell Research, University of Wuerzburg, 97078 Wuerzburg.
| |
Collapse
|
17
|
Lewandrowski U, Zahedi RP, Moebius J, Sickmann A. [Functional proteome analysis of human platelets]. Hamostaseologie 2007; 27:241-245. [PMID: 17938761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023] Open
Abstract
Platelets are anucleated cells and therefore ideal research objects for modern proteome analyses. Despite their importance in thrombosis and hemostasis the protein content of platelets is still poorly characterized in major parts. In preparation for bioinformatic and functional studies a series of proteomic analyses was conducted for platelet subproteomes as well as for posttranslational modifications. Thereby, the identification of 489 proteins, over 550 phosphorylations and 326 N-glycosylation sites was possible, which were not identified in previous proteome studies of platelets. Those results represent new research possibilities for functional characterization of platelet proteins as well as their modifications.
Collapse
Affiliation(s)
- U Lewandrowski
- Rudolf-Virchow-Zentrum für Experimentelle Biomedizin, Universität Würzburg
| | | | | | | |
Collapse
|
18
|
Reinders J, Wagner K, Zahedi RP, Stojanovski D, Eyrich B, van der Laan M, Rehling P, Sickmann A, Pfanner N, Meisinger C. Profiling phosphoproteins of yeast mitochondria reveals a role of phosphorylation in assembly of the ATP synthase. Mol Cell Proteomics 2007; 6:1896-906. [PMID: 17761666 DOI: 10.1074/mcp.m700098-mcp200] [Citation(s) in RCA: 132] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Mitochondria are crucial for numerous cellular processes, yet the regulation of mitochondrial functions is only understood in part. Recent studies indicated that the number of mitochondrial phosphoproteins is higher than expected; however, the effect of reversible phosphorylation on mitochondrial structure and function has only been defined in a few cases. It is thus crucial to determine authentic protein phosphorylation sites from highly purified mitochondria in a genetically tractable organism. The yeast Saccharomyces cerevisiae is a major model organism for the analysis of mitochondrial functions. We isolated highly pure yeast mitochondria and performed a systematic analysis of phosphorylation sites by a combination of different enrichment strategies and mass spectrometry. We identified 80 phosphorylation sites in 48 different proteins. These mitochondrial phosphoproteins are involved in critical mitochondrial functions, including energy metabolism, protein biogenesis, fatty acid metabolism, metabolite transport, and redox regulation. By combining yeast genetics and in vitro biochemical analysis, we found that phosphorylation of a serine residue in subunit g (Atp20) regulates dimerization of the mitochondrial ATP synthase. The authentic phosphoproteome of yeast mitochondria will represent a rich source to uncover novel roles of reversible protein phosphorylation.
Collapse
Affiliation(s)
- Jörg Reinders
- Rudolf Virchow Center/Deutsche Forschungsgemeinschaft Research Center for Experimental Biomedicine, Universität Würzburg, D-97078 Würzburg, Germany
| | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Zahedi RP, Sickmann A, Boehm AM, Winkler C, Zufall N, Schönfisch B, Guiard B, Pfanner N, Meisinger C. Proteomic analysis of the yeast mitochondrial outer membrane reveals accumulation of a subclass of preproteins. Mol Biol Cell 2006; 17:1436-50. [PMID: 16407407 PMCID: PMC1382330 DOI: 10.1091/mbc.e05-08-0740] [Citation(s) in RCA: 167] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Mitochondria consist of four compartments-outer membrane, intermembrane space, inner membrane, and matrix--with crucial but distinct functions for numerous cellular processes. A comprehensive characterization of the proteome of an individual mitochondrial compartment has not been reported so far. We used a eukaryotic model organism, the yeast Saccharomyces cerevisiae, to determine the proteome of highly purified mitochondrial outer membranes. We obtained a coverage of approximately 85% based on the known outer membrane proteins. The proteome represents a rich source for the analysis of new functions of the outer membrane, including the yeast homologue (Hfd1/Ymr110c) of the human protein causing Sjögren-Larsson syndrome. Surprisingly, a subclass of proteins known to reside in internal mitochondrial compartments were found in the outer membrane proteome. These seemingly mislocalized proteins included most top scorers of a recent genome-wide analysis for mRNAs that were targeted to mitochondria and coded for proteins of prokaryotic origin. Together with the enrichment of the precursor form of a matrix protein in the outer membrane, we conclude that the mitochondrial outer membrane not only contains resident proteins but also accumulates a conserved subclass of preproteins destined for internal mitochondrial compartments.
Collapse
Affiliation(s)
- Rene P Zahedi
- Rudolf-Virchow-Center for Experimental Biomedicine, Universität Würzburg, D-97078 Würzburg, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|